Yeast mitochondrial DNA (mtDNA) is known to code for 3 subunits of cytochrome oxidase, 2-4 subunits of the ATPase and the apocytochrome b. The present studies were undertaken with the aim of sequencing regions of mtDNA with genetic markers of the ATPase and cytochrome b. The gene regions have been purified from rho negative mutants that are known to amplify different segments of the wild type genome. Sequence analysis of the mitochondrial genomes of genetically marked rho negative mutants has provided the nucleotide sequences and amino acid sequences of two ATPase genes and partial sequences of cytochrome b. The three genes utilize a very select set of codons that have almost always an A or T in the third position. The DNA sequence data have also revealed that mitochondria disobey two important rules of the universal code. The terminator UGA is used as a tryptophan codon and the leucine codon CUA is recognized by an unusual threonine tRNA. In addition to these unique coding properties, the mitochondrial genome has been found to have an exceptionally sparse population of genes. Most of the DNA consists of long A+T rich non-coding sequences that do not appear to have any function.